I went through the same dilemma. After finding out about the TSB for this GX470 clunk last year. A little background- we bought a 2004 GX470 with about 58k mi. in June 2008. I debated if I sould get the clunk fixed before it hit 70/72k miles. Since the clunk does not happen every time I stop and was not very severe I decided not to have the fix done.
Some may argue that it is a 'free' repair and I am a fool not to have it done, but I did not want to risk having more things wrong (e.g., the rear suspension, overall ride) AFTER the repair than before.
My suggestion is -- if your 'clunk' is really bad or happens a lot, then get it fixed. If it is only once in a while and you are happy with the overall ride & everything, then you may be better off not doing it.
Also, if your dealer's service dept. is really good & helpful, then you should probably do it -- if anything goes wrong after they will take care of it. BUT, I would have them document (in writing if possible) that there are no other suspension/drive issues BEFORE you do the fix, so if something ELSE is not right after they do it, you can say that it was a direct result of the TSB fix (some places try to say it is unrelated & not caused by their repair, etc.).